Partially disable File Output Node in compositing?
If you output to multiple png files, there is no downside to having separate File Output node for each instead of the one with many inputs. You can then select the ones you want to temporarily disable and press m for mute. If you had multilayer EXR that would be a problem, but since you only need to output separate PNGs, that should work fine. Disconnecting inputs also seems elegant enough for me.

You can also use this new node Switch (Blender 2.80) that you can find in Add -> Layout -> Switch



It gives you a checkbox and you can hit ctrl+h to hide unused inputs when you have it selected as you can see I have done on the first one for it to be more compact. It seems to be animate-able, but I have not tested it.